You are greatly overestimating the amount of work it would take to foil such a system.
I cannot think of a single approach that would be easier for me to write than it would be to defeat. Every system I think of is trivially defeated by anyone even remotely experienced with coding. It only takes one person.
So it's totally not worth the effort.
It's not even about the efforts on the side of the coder(and is more of a side note -- you're no longer simply fetching coords is all). I get that there's no way to significantly hinder development of these kinds of mods, and the "harder to do" part is more in relation to the user and in part depends on how the server operates. For instance, some minecraft servers place you at a random location in the world, which can be anywhere between 200 and 3,000 blocks from spawn when you first join. With no obfuscation and a coordinate mod, you'll know exactly where you are and can instantly begin navigating to a griefer's base to get munitions for the coming storm.
I actually went on a server where the coordinates were "randomized" on Minecraft, once(To be precise, they changed with every teleport, respawn, and login). There weren't many of them around, maybe a couple dozen that used it. One or two big servers did. Teleporting always showed the "loading terrain" screen like you were changing worlds, so all the terrain unloaded before the new terrain at my destination loaded up. On a server like that... it could take hours for you just to find a point of reference, and that's assuming you even go in the right direction. Having some experience with these kinds of gigs, obfuscation on servers like that would be really effective against the users themselves(AKA the ones that picked up a client off of god-knows-where and just like burning houses), since 99% of the time, as a zero-day griefer, you want to go in, blow stuff up, maybe kill a few things, and get outpretty quickly. It's supposed to be something you do in an afternoon for a fair number of people. Having the extra time sink of getting your bearings for what could be the better half of an hour or several hours kills it for the griefers themselves. In a reasonable capacity it depends on the servers and how they decide to introduce new players to the world. A static spawn won't help hinder navigation, of course.
Though, there is one thing that I absolutely hate that can be prevented with this pretty reliably. Let's say there's a town that's legitimately at x:15000 z:22950, and it has a warp portal in the middle of it. The town, naturally, is surrounded by walls and a sealed gate that only townspeople can get through. So, you're enemies with this town and happen to have this fabled coordinates mod. Unobfuscated, you instantly know where to go start building a raid base. When it's obfuscated, you can't leave the city to make a warp gate for your friends to come to, and, of course, all the coordinates you do have are relative to a point of reference that is lost when you teleport to an unknown destination.
TL;DR It's less about making it hard to code against, and more about making it inconvenient enough for people that just join a server to meet up with strangers to get griefing gear that they get bored trying to find the agreed upon point of reference. It prevents people from "coord harvesting" by warping into towns, and although it depends on the server it can be very effective with "zero-day" griefers that join for the sole purpose of griefing through the afternoon.